... then the damage value of the infusion stone is changed and it is no more the same as in the applied recipe. When I put that so changed stone back into the recipe and press "apply" then it works again one time only.

Infusion stone = mystical agriculture

@WebDragon: Thanks for the hint. Will do that as soon as my current world has MA farms.

This works with Mystical Agriculture converting Inferium -> Prudentium -> Intermedium, etc
make two Infusion crystals, one as a zero-use crystal you record and save the recipes with, and one that gets slowly used up over time being held in the system. I did this on sky factory 3 and it worked like a charm

Hard to avoid really

Maybe with an option to ignore the damage value or metadata? But then there are a lot of items which are distinguished with that. Not easy.

Im not sure why McJty of all people would say this is hard to avoid. You simply ignore damage/meta data. This is a common feature of most mods that deal with item manipulation. Whats that about?

I had this issue, but luckily most modpacks with RFTools come with Extra Utilities 2.

Until this is fixed, as a workaround, the the mechanical crafter will work as a substitute, it's not as good as the RFTools crafter, but it does handle infusion stones:

Once you have a master infusion stone, the RFTools crafter might work